def test_andi_netcdf_gcms():
file_path = Path.cwd() / "tests/tests_data/gcms/" / "GCMS_FAMES_01_GCMS-01_20191023.cdf"
reader_gcms = ReadAndiNetCDF(file_path)
reader_gcms.run()
def get_gcms(file_path):
reader_gcms = ReadAndiNetCDF(file_path)
reader_gcms.run()
gcms = reader_gcms.get_gcms_obj()
#gcms.process_chromatogram()
return gcms
def stand_alone():
file_path = get_filename()
reader_gcms = ReadAndiNetCDF(file_path)
reader_gcms.run()
gcms = reader_gcms.get_gcms_obj()
gcms.process_chromatogram()
def get_gcms(file_path, corems_params):
reader_gcms = ReadAndiNetCDF(file_path)
reader_gcms.run()
gcms = reader_gcms.get_gcms_obj()
parameter_from_json.load_and_set_parameters_gcms(
gcms, parameters_path=corems_params)
gcms.process_chromatogram()
return gcms
def run_targetedLF(file_path, ref_file):
Loss_finder = LossFinderTargeted()
reader_gcms = ReadAndiNetCDF(file_path)
reader_gcms.run()
gcms = reader_gcms.get_gcms_obj()
gc_ms = gcms._ms
Loss_finder.noise_cutoff = float(0.85)
Loss_finder.tolerance = float(1)
Loss_finder.ref_file = ref_file
mz_dict, abund = Loss_finder.ms_info_get(gc_ms)
range_ref = Loss_finder.loss_ref_get(ref_file, Loss_finder.tolerance)
mz_filtered, abund_filtered = Loss_finder.threshold_filter(
mz_dict, abund, Loss_finder.noise_cutoff)
offset_hits = Loss_finder.findpeakoffset(range_ref, mz_filtered,
abund_filtered)
#Loss_finder.LF_out(offset_hits, Loss_finder.mz_count)
out = Loss_finder.plot_offset()
print(out)
#ax = gcms.plot_gc_peaks()
#ax.savefig('lf_fig.png')
#ax = MassSpecBase.plot_mz_domain_profile(MassSpecBase)
#plt.show()
#MassSpecBase.plot_mz_domain_profile(gcms)
#MassSpecBase.plot_profile_and_noise_threshold(gcms)
#plt.show()
return offset_hits, Loss_finder.mz_count
def run_targetedLF(file_path, ref_file):
Loss_finder = LossFinderTargeted()
reader_gcms = ReadAndiNetCDF(file_path)
reader_gcms.run()
gcms = reader_gcms.get_gcms_obj()
gc_ms = gcms._ms
Loss_finder.noise_cutoff = float(0.85)
Loss_finder.tolerance = float(2)
Loss_finder.ref_file = ref_file
mz_dict, abund = Loss_finder.ms_info_get(gc_ms)
range_ref = Loss_finder.loss_ref_get(ref_file, Loss_finder.tolerance)
mz_filtered, abund_filtered = Loss_finder.threshold_filter(mz_dict, abund, Loss_finder.noise_cutoff)
offset_hits = Loss_finder.findpeakoffset(range_ref, mz_filtered, abund_filtered)
return offset_hits, Loss_finder.mz_count